The script, however, was well and truly ripped up when a dangerous 31-man move went clear in the opening kilometres. Luckily for Team Sky, second placed rider Michal Kwiatkowski had made it into the move along with Michal Golas. The pair formed part of a group that held on until the finish, with Kwiatkowski winning the stage and bumping Thomas down into second place overall.
It may not have been the initial plan Team Sky had drawn up, but such has been their dominance in Algarve that they conceivably could have claimed up the GC no matter what tactics played out on the final stage to Malhao.
At the finish, Kwiatkowski topped the podium with Thomas second at 1:31 and American Tejay van Garderen (BMC Racing) third at 2:16. The break's success ensured that the showdown between the WorldTour climbers at the race never materialised, with Team Sky picking up three stages out of five throughout the week.
"It was a big break and obviously Kwiatkowski was there. All the other teams were happy, they had guys there and that was it," Thomas said at the finish.
"We kept it around three or four minutes, but nobody wanted to chase for the stage. That was it," he repeated.
The move from Kwiatkowski was not planned, but once the opportunistic Pole was clear, the game plan at Team Sky needed to change. Thomas and his remaining teammates held the break at under four minutes, but with each passing kilometre the pressure switched to Kwiatkowski. If he faltered, then the stage and race could slip from the team's grasp.
"I think we were just following moves, and it just so happened that he went across," Thomas added.
"Nobody really followed, and the gap just went. At least the team won, but for sure I would have liked to have kept the jersey. The form and the legs are still good, so it's a good start to the season.
"The way things were with the numbers in the break, every team just fancied their chances for the stage win. It just happened and that was it."
With the race slipping away from him but Kwiatkowski still winning, Thomas admitted that the last slog up the final climb was mentally tough. At the finish, the Welshman and Kwiatkowski embraced, in a show that proved that there was no ill feeling between them. Thomas could at least console himself with a stage win and second overall.
"It was hard on the head at times, especially the last time up the climb, I was thinking to myself 'what are we racing for?' when people started attacking. I just found out that I'm still on the podium, so that's quite nice I guess."